Climate-driven expansion of blanket bogs in Britain during the Holocene

Blanket bog occupies approximately 6% of the area of the UK today. The Holocene expansion of this hyperoceanic biome has previously been explained as a consequence of Neolithic forest clearance. However, the present distribution of blanket bog in Great Britain can be predicted accurately with a simple model (PeatStash) based on summer temperature and moisture index thresholds, and the same model correctly predicts the highly disjunct distribution of blanket bog worldwide. This finding suggests that climate, rather than land-use history, controls blanket-bog distribution in the UK and everywhere else. We set out to test this hypothesis for blanket bogs in the UK using bioclimate envelope modelling compared with a database of peat initiation age estimates. We used both pollen-based reconstructions and climate model simulations of climate changes between the mid-Holocene (6000 yr BP, 6 ka) and modern climate to drive PeatStash and predict areas of blanket bog. We compiled data on the timing of blanketbog initiation, based on 228 age determinations at sites where peat directly overlies mineral soil. The model predicts that large areas of northern Britain would have had blanket bog by 6000 yr BP, and the area suitable for peat growth extended to the south after this time. A similar pattern is shown by the basal peat ages and new blanket bog appeared over a larger area during the late Holocene, the greatest expansion being in Ireland,Wales, and southwest England, as the model predicts. The expansion was driven by a summer cooling of about 2 °C, shown by both pollen-based reconstructions and climate models. The data show early Holocene (pre- Neolithic) blanket-bog initiation at over half of the sites in the core areas of Scotland and northern England. The temporal patterns and concurrence of the bioclimate model predictions and initiation data suggest that climate change provides a parsimonious explanation for the early Holocene distribution and later expansion of blanket bogs in the UK, and it is not necessary to invoke anthropogenic activity as a driver of this major landscape change.

Using Distributed Temperature Sensing to monitor field scale dynamics of ground surface temperature and related substrate heat flux

We present one of the first studies of the use of Distributed Temperature Sensing (DTS) along fibre-optic cables to purposely monitor spatial and temporal variations in ground surface temperature (GST) and soil temperature, and provide an estimate of the heat flux at the base of the canopy layer and in the soil. Our field site was at a groundwater-fed wet meadow in the Netherlands covered by a canopy layer (between 0-0.5 m thickness) consisting of grass and sedges. At this site, we ran a single cable across the surface in parallel 40 m sections spaced by 2 m, to create a 40×40 m monitoring field for GST. We also buried a short length (≈10 m) of cable to depth of 0.1±0.02 m to measure soil temperature. We monitored the temperature along the entire cable continuously over a two-day period and captured the diurnal course of GST, and how it was affected by rainfall and canopy structure. The diurnal GST range, as observed by the DTS system, varied between 20.94 and 35.08◦C; precipitation events acted to suppress the range of GST. The spatial distribution of GST correlated with canopy vegetation height during both day and night. Using estimates of thermal inertia, combined with a harmonic analysis of GST and soil temperature, substrate and soil-heat fluxes were determined. Our observations demonstrate how the use of DTS shows great promise in better characterising area-average substrate/soil heat flux, their spatiotemporal variability, and how this variability is affected by canopy structure. The DTS system is able to provide a much richer data set than could be obtained from point temperature sensors. Furthermore, substrate heat fluxes derived from GST measurements may be able to provide improved closure of the land surface energy balance in micrometeorological field studies. This will enhance our understanding of how hydrometeorological processes interact with near-surface heat fluxes.

MOLES3: implementing an ISO standards driven data catalogue

ISO19156 Observations and Measurements (O&M) provides a standardised framework for organising information about the collection of information about the environment. Here we describe the implementation of a specialisation of O&M for environmental data, the Metadata Objects for Linking Environmental Sciences (MOLES3). MOLES3 provides support for organising information about data, and for user navigation around data holdings. The implementation described here, “CEDA-MOLES”, also supports data management functions for the Centre for Environmental Data Archival, CEDA. The previous iteration of MOLES (MOLES2) saw active use over five years, being replaced by CEDA-MOLES in late 2014. During that period important lessons were learnt both about the information needed, as well as how to design and maintain the necessary information systems. In this paper we review the problems encountered in MOLES2; how and why CEDA-MOLES was developed and engineered; the migration of information holdings from MOLES2 to CEDA-MOLES; and, finally, provide an early assessment of MOLES3 (as implemented in CEDA-MOLES) and its limitations. Key drivers for the MOLES3 development included the necessity for improved data provenance, for further structured information to support ISO19115 discovery metadata export (for EU INSPIRE compliance), and to provide appropriate fixed landing pages for Digital Object Identifiers (DOIs) in the presence of evolving datasets. Key lessons learned included the importance of minimising information structure in free text fields, and the necessity to support as much agility in the information infrastructure as possible without compromising on maintainability both by those using the systems internally and externally (e.g. citing in to the information infrastructure), and those responsible for the systems themselves. The migration itself needed to ensure continuity of service and traceability of archived assets.

A parallel data assimilation model for oceanographic observations

In this paper we describe the development of a program that aims at the optimal integration of observed data in an oceanographic model describ

Urinary metabolomic profiling to identify biomarkers of a flavonoid-rich and flavonoid-poor fruits and vegetables diet: the FLAVURS trial in adults: the FLAVURS trial

The present study aims to investigate the dose dependent effects of consuming diets enriched in flavonoid-rich and flavonoid-poor fruits and vegetables on the urine metabolome of adults who had a C1.5 fold increased risk of cardiovascular diseases. A single-blind, dose-dependent, parallel randomized controlled dietary intervention was conducted where volunteers (n = 126) were randomly assigned to one of three diets: high flavonoid diet, low flavonoid diet or habitual diet as a control for 18 weeks. High resolution LC– MS untargeted metabolomics with minimal sample cleanup was performed using an Orbitrap mass spectrometer. Putative biomarkers which characterize diets with high and low flavonoid content were selected by state-of-the-art data analysis strategies and identified by HR-MS and HR-MS/MS assays. Discrimination between diets was observed by application of two linear mixedmodels: one including a diet-time interaction effect and the second containing only a time effect. Valerolactones, phenolic acids and their derivatives were among sixteen biomarkers related to the high flavonoid dietary exposure. Four biomarkers related to the low flavonoid diet belonged to the family of phenolic acids. For the first time abscisic acid glucuronide was reported as a biomarker after a dietary intake, however its origins have to be examined by future hypothesis driven experiments using a more targeted approach. This metabolomic analysis has identified a number of dose dependent urinary biomarkers (i.e. proline betaine or iberin-N-acetyl cysteine), which can be used in future observation and intervention studies to assess flavonoids and nonflavonoid phenolic intakes and compliance to fruit and vegetable intervention.

The supernova remnant CTB 37B and its associated magnetar CXOU J171405.7-381031: evidence for a magnetar-driven remnant

We discuss the association between the candidate magnetar CXOU J171405.7-381031 and the supernova remnant CTB 37B. The recent detection of the period derivative of the object allowed an estimation of a young characteristic age of only similar to 1000 yr. This value is too small to be compatible even with the minimum radius of the remnant being >= 10 pc, the value corresponding to the lower limit of the estimated distance of 10.2 +/- 3.5 kpc, unless the true distance happens to be even smaller than the lower limit. We argue that a consistent scenario for the remnant`s origin, in which the latter is powered by the energy injected by a young magnetar, is indeed more accurate to explain the young age, and demonstrates its non-standard (i.e. magnetar-driven) nature.

Comparing detection and location performance of perpendicular and parallel broadside GPR antenna orientations

GPR (Ground Penetrating Radar) results are shown for perpendicular broadside and parallel broadside antenna orientations. Performance in detection and localization of concrete tubes and steel tanks is compared as a function of acquisition configuration. The comparison is done using 100 MHz and 200 MHz center frequency antennas. All tubes and tanks are buried at the geophysical test site of IAG/USP in Sao Paulo city, Brazil. The results show that the long steel pipe with a 38-mm diameter was well detected with the perpendicular broadside configuration. The concrete tubes were better detected with the parallel broadside configuration, clearly showing hyperbolic diffraction events from all targets up to 2-m depth. Steel tanks were detected with the two configurations. However, the parallel broadside configuration was generated to a much lesser extent an apparent hyperbolic reflection corresponding to constructive interference of diffraction hyperbolas of adjacent targets placed at the same depth. Vertical concrete tubes and steel tanks were better contained with parallel broadside antennas, where the apexes of the diffraction hyperbolas better corresponded to the horizontal location of the buried target disposition. The two configurations provide details about buried targets emphasizing how GPR multi-component configurations have the potential to improve the subsurface image quality as well as to discriminate different buried targets. It is judged that they hold some applicability in geotechnical and geoscientific studies. (C) 2009 Elsevier B.V. All rights reserved.

Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

Recurrent submicroscopic genomic copy number changes are the result of nonallelic homologous recombination (NAHR). Nonrecurrent aberrations, however, can result from different nonexclusive recombination-repair mechanisms. We previously described small microduplications at Xq28 containing MECP2 in four male patients with a severe neurological phenotype. Here, we report on the fine-mapping and breakpoint analysis of 16 unique microduplications. The size of the overlapping copy number changes varies between 0.3 and 2.3 Mb, and FISH analysis on three patients demonstrated a tandem orientation. Although eight of the 32 breakpoint regions coincide with low-copy repeats, none of the duplications are the result of NAHR. Bioinformatics analysis of the breakpoint regions demonstrated a 2.5-fold higher frequency of Alu interspersed repeats as compared with control regions, as well as a very high GC content (53%). Unexpectedly, we obtained the junction in only one patient by long-range PCR, which revealed nonhomologous end joining as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array comparative genomic hybridization analysis demonstrated the presence of a second duplicated region more telomeric at Xq28, of which one copy was inserted in between the duplicated MECP2 regions. These data suggest a two-step mechanism in which part of Xq28 is first inserted near the MECP2 locus, followed by breakage-induced replication with strand invasion of the normal sister chromatid. Our results indicate that the mechanism by which copy number changes occur in regions with a complex genomic architecture can yield complex rearrangements.

Retinoic acid inhibits dendritic cell differentiation driven by interleukin-4

All-trans-retinoic acid (atRA) appears to affect Th1-Th2 differentiation and its effects on immune responses might also be mediated by dendritic cell (DC). Nonetheless, studies have been showing contradictory results since was observed either induction or inhibition of DC differentiation. Our aim was to investigate atRA action on human monocyte derived DC differentiation. For this purpose we tested pharmacological and physiological doses of atRA with or without cytokines. Cell phenotypes were analyzed by flow cytometry and function was investigated by phagocytosis and respiratory burst. DC, positive control group, was differentiated with GM-CSF and IL-4 and maturated with TNF-alpha. We demonstrated that atRA effects depend on the dose used as pharmacological doses inhibited expression of all phenotypic markers tested while a physiological dose caused cell differentiation. However, atRA combined or not with cytokines did not promote DC differentiation. In fact, atRA was detrimental on IL-4 property as a DC inductor. (C) 2009 Elsevier Inc. All rights reserved.

Development of an adenoviral vector with robust expression driven by p53

Here we introduce a new adenoviral vector where transgene expression is driven by p53. We first developed a synthetic promoter, referred to as PGTx beta containing a p53-responsive element, a minimal promoter and the first intron of the rabbit P-globin gene. Initial assays using plasmid-based vectors indicated that expression was tightly controlled by p53 and was 5-fold stronger than the constitutive CMV immediate early promoter/enhancer. The adenoviral vector, AdPG, was also shown to offer p53-responsive expression in prostate carcinoma cells LNCaP (wt p53), DU-145 (temperature sensitive mutant of p53) and PC3 (p53-null, but engineered to express temperature-sensitive p53 mutants). AdPG served as a sensor of p53 activity in LNCaP cells treated with chemotherapeutic agents. Since p53 can be induced by radiotherapy and chemotherapy, this new vector could be further developed for use in combination with conventional therapies to bring about cooperation between the genetic and pharmacologic treatment modalities. (c) 2007 Elsevier Inc. All rights reserved.

Preventive and curative glycoside kaempferol treatments attenuate the TH2-driven allergic airway disease

Asthma is a chronic respiratory disease characterized by airway inflammation and airway hyperresponsiveness (AHR). One strategy to treat allergic diseases is the development of new drugs. Flavonoids are compounds derived from plants and are known to have antiallergic, anti-inflammatory, and antioxidant properties. To investigate whether the flavonoid kaempferol glycoside 3-O-[beta-D-glycopiranosil-(1 -> 6)-alpha-L-ramnopiranosil]-7-O-alpha-L-ramnopiranosil-kaempferol (GRRK) would be capable of modulating allergic airway disease (AAD) either as a preventive (GRRK P) or curative (GRRK C) treatment in an experimental model of asthma. At weekly intervals, BALB/c mice were subcutaneously (sc) sensitized twice with ovalbumin (OVA)/alum and challenged twice with OVA administered intranasally. To evaluate any preventive effects GRRK was administered 1 h (hour) before each OVA-sensitization and challenge, while to analyze the curative effects mice were first sensitized with OVA, followed by GRRK given at day 18 through 21. The onset: of AAD was evaluated 24 h after the last OVA challenge. Both treatments resulted in a dose-dependent reduction in total leukocyte and eosinophil counts in the bronchoalveolar lavage fluid (BAL). GRRK also decreased CD4(+), B220(+), MHC class II and CD40 molecule expressions in BAL cells. Histology and lung mechanic showed that GRRK suppressed mucus production and ameliorated the AHR induced by OVA challenge. Furthermore, GRRK impaired Th2 cytokine production (IL-5 and IL-13) and did not induce a Th1 pattern of inflammation. These findings demonstrate that GRRK treatment before or after established allergic lung disease down-regulates key asthmatic features. Therefore. GRRK has a potential clinical use for the treatment of allergic asthma. (C) 2009 Elsevier B.V. All rights reserved.

An approach for solving the lot-sizing problem of a market-driven foundry

Foundries can be found all over Brazil and they are very important to its economy. In 2008, a mixed integer-programming model for small market-driven foundries was published, attempting to minimize delivery delays. We undertook a study of that model. Here, we present a new approach based on the decomposition of the problem into two sub-problems: production planning of alloys and production planning of items. Both sub-problems are solved using a Lagrangian heuristic based on transferences. An important aspect of the proposed heuristic is its ability to take into account a secondary practice objective solution: the furnace waste. Computational tests show that the approach proposed here is able to generate good quality solutions that outperform prior results. Journal of the Operational Research Society (2010) 61, 108-114. doi:10.1057/jors.2008.151

A Parallel Hardware Architecture for Scale and Rotation Invariant Feature Detection

This paper proposes a parallel hardware architecture for image feature detection based on the Scale Invariant Feature Transform algorithm and applied to the Simultaneous Localization And Mapping problem. The work also proposes specific hardware optimizations considered fundamental to embed such a robotic control system on-a-chip. The proposed architecture is completely stand-alone; it reads the input data directly from a CMOS image sensor and provides the results via a field-programmable gate array coupled to an embedded processor. The results may either be used directly in an on-chip application or accessed through an Ethernet connection. The system is able to detect features up to 30 frames per second (320 x 240 pixels) and has accuracy similar to a PC-based implementation. The achieved system performance is at least one order of magnitude better than a PC-based solution, a result achieved by investigating the impact of several hardware-orientated optimizations oil performance, area and accuracy.